biostudies-literatureWaszkiewicz RNSFNational Science Center of PolandUniversity of Texasthe Canadian Natural Science and Engineering Research CouncilCanada Foundation for InnovationNational Institutes of HealthNIGMS NIH HHSNational Science FoundationCanada 150 Research Chairs4027-4042https://www.ebi.ac.uk/biostudies/studies/S-EPMC10164573biostudies-literatureUnknown51(8)DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we appliNucleic acids researchDNA supercoiling-induced shapes alter minicircle hydrodynamic properties.PMC10164573UMO-2018/31/B/ST8/03640DG-RGPIN-2019-05637R01 GM1206001R01GM120600R35 GM1417932018/31/D/ST3/02408C150-2017-00015TG-MCB070039NTG457201CFI-37589MCB 2107527Lisicki MFogg JMZechiedrich LWaszkiewicz RDemeler BEkiel-Jezewska MLRanasinghe MSzymczak PCatanese DJfalseDNA supercoiling-induced shapes alter minicircle hydrodynamic properties.DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we appli2023-01-01T00:00:00Z2023 May2025-04-26T14:29:45.776Z2025-04-06T14:35:05.026ZS-EPMC101645733697111010.1093/nar/gkad183